Fiji/ImageJ2 plugins for low-energy electron microscopy (LEEM) and x-ray photoemission electron microscopy (PEEM), in particular for instruments from Elmitec running the U-view 2002 software.

Registers the Elmitec UKSOFT2000 format (.dat extension) with SCIFIO, allowing files to be opened directly via File > Open or drag-and-drop in Fiji. Single images only; multi-image files are not supported. However, it is not too fast, due to the overhead of reading all the fields. For long series of images, it is (much) faster to use the specific UView Folder Reader (see below).

Metadata stored in the file header (start voltage, temperature, pressure, field of view, micrometer position, date, etc.) is attached to the dataset and visible via Image > Show Info.

Both leemdataversion variants are supported: version > 2 (external LEEM data block after the image header) and versions 1–2 (LEEM data embedded inside the image header).

Plugins > LEEMandPEEM > UView Folder Reader

Opens a folder of .dat files as an ImageJ stack. A dialog allows filtering by filename substring and selecting a range and increment (options are remembered between runs). Each slice label contains the metadata extracted from that file's header in key=value format, which can be used by Plot Intensity vs Tag.

If the folder contains a CSV file whose name does not include the word meta, the plugin reads it and merges its per-image metadata into the stack. The rows of the CSV are matched to the .dat files by position (both sorted alphabetically), so the first data row corresponds to the first image, and so on.

The following columns are recognised and added as slice label tags:

This matches the metadata CSV format produced by the PEEM data acquisition system at the Solaris DEMETER beamline, where each XAS/NEXAFS scan folder contains a CSV file with one row per image alongside columns for photon energy, flux monitors, and other beamline parameters. A typical file looks like:

Energy,ROI1_Intensity,ROI2_Intensity,...,M4b,...
520.024,34.16,...,5875.16,...
520.501,34.15,...,5901.09,...
...

Both comma- and semicolon-delimited files are supported. UTF-8 BOM (added by Excel on Windows) is stripped automatically.

Once loaded, Energy (eV) and M4b appear in the Plot Intensity vs Tag tag dropdowns alongside the metadata embedded in the .dat files themselves.

Plugins > LEEMandPEEM > Plot Intensity vs Tag

Plots the mean intensity of each slice in a stack against a metadata value embedded in the slice labels. Typical use: plot intensity vs. start voltage (IV curve) or photon energy (XAS/NEXAFS spectrum).

Features:

• X tag dropdown — lists all numeric metadata fields found in the slice labels; includes Frame Number as a fallback. X axis label is pre-filled from the tag name (editable, e.g. rename to Binding Energy (eV) for XPS)
• X formula — optional expression applied to the tag values before plotting (x = tag value; e.g. 350 - x, x * 0.001)
• Y tag + Y formula — optional second tag and formula for transforming the intensity (y = mean intensity, t = Y tag value). Typical use: y / t with M4b as the Y tag to normalise by beamline flux
• Multi-ROI plotting — if the ROI Manager is open, one curve is plotted per ROI with a legend; selected ROIs in the manager are used, otherwise all. Without the ROI Manager the active ROI (or whole frame) is used
• Save CSV — checkbox to export the plot data (X column + one column per ROI) to a CSV file, ready for further analysis in Python or other tools
• All dialog choices are remembered between runs via ij.Prefs

Plugins > LEEMandPEEM > Process Spectrum

Post-processes an active plot window produced by Plot Intensity vs Tag. Operations applied in order:

1. Pre-edge subtraction — subtracts the average intensity around a chosen energy
2. Post-edge normalisation — divides by the average intensity around a second chosen energy
3. Difference — curve 1 minus curve 2 (available when the plot has two or more curves)

Each energy value is averaged over the five nearest points for robustness against noise. The processed curves are shown in a new plot window. All settings are remembered between runs.

Plugins > LEEMandPEEM > Quick Normalize

One-shot beamtime command that chains Plot Intensity vs Tag and Process Spectrum using their last-used settings, with no dialogs. Configure both plugins once on a representative dataset, then run Quick Normalize on every subsequent dataset for an instant normalised spectrum. Results are logged to the Fiji log window.

1. Open the scan folder with UView Folder Reader. If the beamline CSV is present, Energy (eV) and M4b are automatically added to every slice.
2. Draw one or more ROIs on the stack (use the ROI Manager for multiple regions).
3. Run Plot Intensity vs Tag:
   • Set X tag to Energy (eV).
   • Set Y tag to M4b and Y formula to y / t to normalise the intensity by the incident flux.
   • With multiple ROIs open, all curves are overlaid on the same plot with a legend.
4. Run Process Spectrum on the resulting plot:
   • Set a pre-edge energy (flat region before the absorption edge) and a post-edge energy (region above the edge).
   • Enable Pre-edge subtraction and Post-edge normalisation to obtain a normalised NEXAFS spectrum (0 before edge, 1 after edge).
   • Optionally enable Difference to compute the XMCD signal (two-ROI or two-curve plots).
5. For subsequent datasets at the same beamline, run Quick Normalize directly — it reuses the tag, formula, and energy settings from the previous run with no dialogs.
6. Check Save CSV in Plot Intensity vs Tag to export raw curves for further processing, e.g. with Python/matplotlib.

Copy LEEMandPEEM-<version>.jar from target/ into the plugins/ folder of your Fiji installation and restart Fiji.

Requires Maven and Java 11+.

mvn clean package

The jar will be in target/.

• Fiji with SCIFIO 0.45 or later (included in current Fiji releases)
• pom-scijava 34.1.0

Magnetic vector field analysis (OVF format I/O, XYZ reconstruction, spherical conversion) has moved to MagneticHelper.

GNU General Public License v2.0 — see LICENSE.txt.

Juan de la Figuera, IQFR-CSIC (http://surfmoss.iqfr.csic.es)